After negotiations with the Klingons break down, the Enterprise is sent to block Klingon expansionism on the Class M planet Organia, described by Spock as class D- on the ``Richter scale of culture.'' After being attacked, the Enterprise destroys a Klingon vessel. Shortly thereafter, Uhura reports that a state of war has been declared between the Federation and the Klingons. The Enterprise then enters orbit around Organia, despite the warning from Unit XY75847 that a fleet of Klingon ships is in their sector.
Spock and Kirk beam down to the planet Organia to warn the populace of an impending Klingon invasion. Strangely, the Organians do not appear the least concerned about strangers beaming down in their midst, and do not appear the least worried by the prospect of Klingon occupation. Ayelborne, Chairman of the Council of Elders, greets them and invites Kirk to speak to the council. Kirk offer protection from the Klingons, but Ayelborne says his people have no need of defenses and are in no danger. This laissez-faire attitude seems consistent with a report from Spock that the society of Organia has been completely stagnant for tens of thousands of years.
In the meantime, the Klingon fleet arrives and Sulu is forced to warp the Enterprise out of the vicinity, stranding Kirk and Spock. A party of heavily armed Klingons then beams down, according to one of the elders, despite the fact that Spock's tricorder has no way of ascertaining this. The Organians disguise Kirk and Spock as natives in an attempt to protect them from harm at the Klingons' hands.
Ayelborne bids welcome to the Klingon Kor, who declares himself military governor of Organia, and claims that Kirk is Barona, one of Organia's leading citizens. Spock is harder to explain, but claims he is a dealer in kevis and trillium. Kor finds Kirk's lack of complacency and obvious hatred of the Klingons refreshing on a planet otherwise filled with passive Organians, and declares him liaison between the Klingons and the people of Organia. Despite force 4 scanning of Kirk's mind by a Klingon mind-probe device, Spock is able to maintain his merchant pretext and is allowed to go free.
Kirk and Spock attempt to interfere with the Klingon occupation and incite the natives to defend themselves by blowing up a Klingon munitions dump. When Kirk admits what he has done to Ayelborne, he is admonished. Unfortunately, Kor has bugged the Council chambers and prepares to mind-probe Kirk and then execute him. However, Ayelborne declares that this is unnecessary, since Barona's true identity is actually James T. Kirk of the Starship Enterprise.
Kor then threatens to fry Kirk's mind and dissect Spock to find how he is capable of foiling the mind scanner unless Kirk tells him all he wants to know. He is given 12 hours, and thrown into a cell with Spock in the meantime. However, Ayelborne lets them out, despite the fact that the Klingons are vigorously guarding the cell and observe nothing. As revenge, the Klingons initiate mass executions of 200 Organians, and threaten to kill 200 more every 2 hours unless the escaped prisoners are returned. However, the Organians continue to insist on non-violence. Kirk then threatens physical injury to Ayelborne unless he returns their phasers, which he wants to use in a two-man suicide attack against the Klingons. Ayelborne is shocked by Kirk's behavior, but agrees to let him have the phasers.
Spock reports that the odds of them returning alive from their mission are 7824.7:1. They begin by killing two Klingon guards, then waylay and pump another Klingon for information. Spock reports that their odds of surviving have now improved to 7000:1. Kirk and Spock manage to take Kor prisoner just as the Federation and Klingon fleets are massing for attack in the Organian system.
At this point, the Organian council brings all weapons and instruments of violence to a temperature of 350 degrees, including those on the Enterprise. Ayelborne then immobilize all fighting forces of both sides, producing an immediate cessation of hostilities which the Federation and Klingons subsequently maintain. Ayelborne also reports that in the future, Klingons and Earthlings will be allies, a prediction that is not bourn out until the Star Trek IV movie and Star Trek, The Next Generation television series. It turns out that the Organians are actually advanced beings capable of creating illusions, and so were never actually inconvenienced by the Klingons to start with. Spock notes that the Organians are as far above humans on the evolutionary scale as humans are above the amoeba.